US-EC Workshop on Marine Genomics, Washington DC fall 2010
Training the
next generation of Biologists
Roderic Guigó, roderic.guigo@crg.cat
Center for Genomic Regulation, Barcelona
http://bioinformatica.upf.edu/
disclaimers
• University Pompeu Fabra
– Ranks 155 in the world (Times Higher
Education)
– Only two spanish universitites among the
top 200. (Univeristy of Barcelona, 142)
• Disparity between the American and
European undergraduate systems
• Disparity even within European
countries
– Bologna process
Bologna process
• The purpose of the Bologna Process is to create the
European Higher Education Area by making academic
degree standards and quality assurance standards more
comparable and compatible throughout Europe
– 1st cycle: typically 180−240 ECTS credits, usually awarding
a Bachelor's degree. 3 years
– 2nd cycle: typically 90−120 ECTS credits (a minimum of 60
on 2nd-cycle level). Usually awarding a Master's degree. 2
years
– 3rd cycle: Doctoral degree. No ECTS range given. 3 years,
aprox.
Why “next generation biologists”
should be trained differently than
biologists of previous generations?
Why “next generation biologists”
should be trained differently than
biologists of previous generations?
• The impact of technology
– in the way we do Biology
Technology is not
new to Biology
In 1676 his credibility was questioned
when he sent the Royal Society a copy
of his first observations of microscopic
single celled organisms. Heretofore,
the existence of single celled
organisms was entirely unknown …
The Royal Society arranged to send an
English vicar, as well as a team of
respected jurists and doctors to Delft,
Holland to determine whether it was in
fact Van Leeuwenhoek's ability to
observe and reason clearly (wikipedia)
Two moments in the second
half of the past century
1. Sequencing (Sanger et al)
ACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACGG
GGATGAGCTCAGGGGCCTCTAGAAAGATGTAGCTGGGACCTCGGGAAGCCCTGGCCTCCAGGTAGTCTCAG
GAGAGCTACTCAGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCCAGCAGCAGGGGACTGGAC
CTGGGAAGGGCTGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCATGTGGACTA
GGAGCTAAGCCACAGCAGGACCCCCACGAGTTGTCACTGTCATTTATCGAGCACCTACTGGGTGTCCCCAG
TGTCCTCAGATCTCCATAACTGGGAAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTT
AAAATGAGGACTGAATTAGCTCATAAATGGAAAACGGCGCTTAAATGTGAGGTTAGAGCTTAGAATGTGAAG
GGAGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGAGGGGGTGTGGAAT
TTGAACCCCGGGAGAGAAAGATGGAATTTTGGCTATGGAGGCCGACCTGGGGATGGGGAAATAAGAGAAG
ACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAACTGTTTGTGCTGGGATTAGGCTGTT
GCAGATAATGGAGCAAGGCTTGGAAGGCTAACCTGGGGTGGGGCCGGGTTGGGGTCGGGCTGGGGGCGG
GAGGAGTCCTCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATG
AAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGCGGGGCTTGCTCGGTTTTCCCCG
CTTCTCCCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAAGCACACCCTGGGCCCCCTCTTCTTCTGC
TGGTCTGTCCCCTGAGGGGAAAGCCCAGGTCTGAGGCTTCTATGCTGCTTTCTGGCTCAGAACAGCGATTTG
ACGCTCTGTGAGCCTCGGTTCCTCCCCCGCTTTTTTTTTTTCAGCCAGAGTCTCACTCTGTCGCCCAGGCTG
GAGTGCAGTGGCGCAATCTCAGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCTATTCTCCCGCCTCAGC
CTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCCGGCTAATTTTTTGTACTTTGAGTAGGGAAGG
GGTTTCACTGTATTATCCAGGATGGTCTCTATCTCCTGACCTCGTGATCTGCCCGCCTGGCCTCCCAAAGTGC
TGGAATTACAGGCGTGAGCCTCCGCGCCCGGCCTCCCCATCCTTAATATAGGAGTTAGAAGTTTTTGTTTGTT
TGTTTTGTTTTGTTTTTGTTTTGTTTTGAGATGAAGTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCTCCCA
Two moments in the second
half of the past century
2. mutliplexing, automating,…
– Surveying many things at once
– Surveying whole systems
From analytic to syntetic
Biology is transitioning (at least partially)
from
an “analytic” science: the real world is
disected in its elemental components in order to
be comprehended
to
“syntetic” science: the challenge is the
integration of globlal information on the living
cell/individual/population/(eco)sytem.
From data acquisition to
data analysis
Biology, a science in which the effort has
traditionally been directed towards data
aquisition has become in a very short time a
discipline in which the data is obtained with
almost no human intervention, and the effort
is turning towards data analysis.
DNA microarrays
March 24, 2016
13
In summary
• Intrinsec symbolic/computational nature
of biological (genomic) data
• Emphasis in synthesis (rather/in
addition to analysis)
• Exponential data production
– Separated from human intervention
Bioinformatics, Genomics,
Systems Biology in Medline
Bioinformatics
Google search: X-informatics (11 juny, 2007)
bioinformatics
chemoinformatics
astroinformatics
neuroinformatics
socioinformatics
geoinformatics
meteoinformatics
econoinformatics
ecoinformatics
14,100,000
226,000
195
364,000
610
506,000
48
441
160,000
Engineering and biology:
increasingly interconnected
• Improved technologies to survey Biological
Systems
– NGS and the like
[technological fluency]
• Engineering of Biological Systems
– Medicine
– New and modified biological systems
• Using Biology to build non-biological systems
– DNA computing
Biology has changed and it
is changing
• Quantitative thinking
• Ability to attack
unanticipated problems
Biology requires
quantitative thinking
•
•
•
•
Statistics
Mathematics
Computer Science
…
and programming skills
(unix)
• The ability to interrogate data, and to
models systems
Biology is not anymore
softer than other hard
sciences
• We do not know the problems that our
future biologists will have to address,
and what competences will be
important for them. But
– Competences required are likely to be very
heterogeneous
Training the
next generation of
Biologists Scientists
What Is the
Integrated Science Curriculum?
The curriculum covers the core material of introductory physics,
chemistry, biology (genetics and biochemistry), and computer science,
all in an integrated manner. The central role of mathematics as a
universal language of science is emphasized throughout. In every area
of science, students learn in part through quantitative problem solving;
to this end computational methods are taught and integrated into the
entire program.
Collaborative problem solving is stressed over memorization and
regurgitation of facts. Close contact between students and faculty is a
major feature of the new curriculum; class sizes are kept small.
Identification of selenoproteins
in the genomes of protists
SelU
Changes in sociology of
science
Internet and Information Technology is
changing sociology of Science
• Small individual projects transitioning to
large-scale multi-site projects
– Distributed expertise
• Diffuse, geographically disperse, dynamically
evolving group of colleagues
• Virtual communication (over the phone,
internet) increasingly important
– ENCODE. I have a minimum of 4 conference calls
a week (including groups from California, East
Cost, Europe, Singapore, Japan)
Changes in the way we
communicate with other
(human) colleagues
• Collaborative problem solving over the
Internet
– Students in different places (ideally with
complementary expertise) working
together to solve the same problem
Learning to communicate with
non-human intelligent agents
• Data grows super-exponentially
• Computers grows exponentially
• People grow linearly (at the best)
=> Increasingly large fraction of scientific
activity left to the machines.
Training in biology to nonbiologists
• Law
• International and National Policy (bioterrorism,climate change,biodiversity,…)
• Forensic
• History, Arqueology
• Arquitecture, …
Summary
• Quantitative thinking is essential
– But do not forget Natural History
• Programming as important and lab skills
• Ultra specialization is bad
– We can not anticipate the relevant problems
– Follow Integrative Science approaches
• Collaborative work will take precedence over
individual work
– Teach communication skills over virtual communities
of colleagues
– Communication with non-human intelligent agents
• Emergence of Biological technologies